The DBCLS BioHackathon: Standardization and interoperability for bioinformatics web services and workflows

Toshiaki Katayama; Kazuharu Arakawa; Mitsuteru Nakao; Keiichiro Ono; Kiyoko F. Aoki-Kinoshita; Yasunori Yamamoto; Atsuko Yamaguchi; Shuichi Kawashima; Hong Woo Chun; Jan Aerts; Bruno Aranda; Lord H. Barboza; Raoul J.P. Bonnal; Richard Bruskiewich; Jan C. Bryne; José M. Fernández; Akira Funahashi; Paul M.K. Gordon; Naohisa Goto; Andreas Groscurth; Alex Gutteridge; Richard Holland; Yoshinobu Kano; Edward A. Kawas; Arnaud Kerhornou; Eri Kibukawa; Akira R. Kinjo; Michael Kuhn; Hilmar Lapp; Heikki Lehvaslaiho; Hiroyuki Nakamura; Yasukazu Nakamura; Tatsuya Nishizawa; Chikashi Nobata; Tamotsu Noguchi; Thomas M. Oinn; Shinobu Okamoto; Stuart Owen; Evangelos Pafilis; Matthew Pocock; Pjotr Prins; René Ranzinger; Florian Reisinger; Lukasz Salwinski; Mark Schreiber; Martin Senger; Yasumasa Shigemoto; Daron M. Standley; Hideaki Sugawara; Toshiyuki Tashiro; Oswaldo Trelles; Rutger A. Vos; Mark D. Wilkinson; William York; Christian M. Zmasek; Kiyoshi Asai; Toshihisa Takagi

doi:10.1186/2041-1480-1-8

The DBCLS BioHackathon: Standardization and interoperability for bioinformatics web services and workflows

Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F. Aoki-Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Shuichi Kawashima, Hong Woo Chun, Jan Aerts, Bruno Aranda, Lord H. Barboza, Raoul J.P. Bonnal, Richard Bruskiewich, Jan C. Bryne, José M. Fernández, Akira Funahashi, Paul M.K. Gordon, Naohisa Goto, Andreas GroscurthAlex Gutteridge, Richard Holland, Yoshinobu Kano, Edward A. Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R. Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehvaslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M. Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew Pocock, Pjotr Prins, René Ranzinger, Florian Reisinger, Lukasz Salwinski, Mark Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M. Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A. Vos, Mark D. Wilkinson, William York, Christian M. Zmasek, Kiyoshi Asai, Toshihisa Takagi

Research output: Contribution to journal › Review article › peer-review

25 Citations (Scopus)

Abstract

Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.

Original language	English
Article number	8
Journal	Journal of Biomedical Semantics
Volume	1
DOIs	https://doi.org/10.1186/2041-1480-1-8
Publication status	Published - 2010 Aug 21
Externally published	Yes

ASJC Scopus subject areas

Information Systems
Computer Science Applications
Health Informatics
Computer Networks and Communications

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10.1186/2041-1480-1-8

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Katayama, T., Arakawa, K., Nakao, M., Ono, K., Aoki-Kinoshita, K. F., Yamamoto, Y., Yamaguchi, A., Kawashima, S., Chun, H. W., Aerts, J., Aranda, B., Barboza, L. H., Bonnal, R. J. P., Bruskiewich, R., Bryne, J. C., Fernández, J. M., Funahashi, A., Gordon, P. M. K., Goto, N., ... Takagi, T. (2010). The DBCLS BioHackathon: Standardization and interoperability for bioinformatics web services and workflows. Journal of Biomedical Semantics, 1, [8]. https://doi.org/10.1186/2041-1480-1-8

Katayama, T, Arakawa, K, Nakao, M, Ono, K, Aoki-Kinoshita, KF, Yamamoto, Y, Yamaguchi, A, Kawashima, S, Chun, HW, Aerts, J, Aranda, B, Barboza, LH, Bonnal, RJP, Bruskiewich, R, Bryne, JC, Fernández, JM, Funahashi, A, Gordon, PMK, Goto, N, Groscurth, A, Gutteridge, A, Holland, R, Kano, Y, Kawas, EA, Kerhornou, A, Kibukawa, E, Kinjo, AR, Kuhn, M, Lapp, H, Lehvaslaiho, H, Nakamura, H, Nakamura, Y, Nishizawa, T, Nobata, C, Noguchi, T, Oinn, TM, Okamoto, S, Owen, S, Pafilis, E, Pocock, M, Prins, P, Ranzinger, R, Reisinger, F, Salwinski, L, Schreiber, M, Senger, M, Shigemoto, Y, Standley, DM, Sugawara, H, Tashiro, T, Trelles, O, Vos, RA, Wilkinson, MD, York, W, Zmasek, CM, Asai, K & Takagi, T 2010, 'The DBCLS BioHackathon: Standardization and interoperability for bioinformatics web services and workflows', Journal of Biomedical Semantics, vol. 1, 8. https://doi.org/10.1186/2041-1480-1-8

@article{cbe03ac5edad4912aa575cf7e88222ef,

title = "The DBCLS BioHackathon: Standardization and interoperability for bioinformatics web services and workflows",

abstract = "Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.",

author = "Toshiaki Katayama and Kazuharu Arakawa and Mitsuteru Nakao and Keiichiro Ono and Aoki-Kinoshita, {Kiyoko F.} and Yasunori Yamamoto and Atsuko Yamaguchi and Shuichi Kawashima and Chun, {Hong Woo} and Jan Aerts and Bruno Aranda and Barboza, {Lord H.} and Bonnal, {Raoul J.P.} and Richard Bruskiewich and Bryne, {Jan C.} and Fern{\'a}ndez, {Jos{\'e} M.} and Akira Funahashi and Gordon, {Paul M.K.} and Naohisa Goto and Andreas Groscurth and Alex Gutteridge and Richard Holland and Yoshinobu Kano and Kawas, {Edward A.} and Arnaud Kerhornou and Eri Kibukawa and Kinjo, {Akira R.} and Michael Kuhn and Hilmar Lapp and Heikki Lehvaslaiho and Hiroyuki Nakamura and Yasukazu Nakamura and Tatsuya Nishizawa and Chikashi Nobata and Tamotsu Noguchi and Oinn, {Thomas M.} and Shinobu Okamoto and Stuart Owen and Evangelos Pafilis and Matthew Pocock and Pjotr Prins and Ren{\'e} Ranzinger and Florian Reisinger and Lukasz Salwinski and Mark Schreiber and Martin Senger and Yasumasa Shigemoto and Standley, {Daron M.} and Hideaki Sugawara and Toshiyuki Tashiro and Oswaldo Trelles and Vos, {Rutger A.} and Wilkinson, {Mark D.} and William York and Zmasek, {Christian M.} and Kiyoshi Asai and Toshihisa Takagi",

note = "Funding Information: BioHackathon 2008 is financially supported by the Integrated Database Project, Ministry of Education, Culture, Sports, Science and Technology of Japan and the Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology, Japan.",

year = "2010",

month = aug,

day = "21",

doi = "10.1186/2041-1480-1-8",

language = "English",

volume = "1",

journal = "Journal of Biomedical Semantics",

issn = "2041-1480",

publisher = "BioMed Central",

}

TY - JOUR

T1 - The DBCLS BioHackathon

T2 - Standardization and interoperability for bioinformatics web services and workflows

AU - Katayama, Toshiaki

AU - Arakawa, Kazuharu

AU - Nakao, Mitsuteru

AU - Ono, Keiichiro

AU - Aoki-Kinoshita, Kiyoko F.

AU - Yamamoto, Yasunori

AU - Yamaguchi, Atsuko

AU - Kawashima, Shuichi

AU - Chun, Hong Woo

AU - Aerts, Jan

AU - Aranda, Bruno

AU - Barboza, Lord H.

AU - Bonnal, Raoul J.P.

AU - Bruskiewich, Richard

AU - Bryne, Jan C.

AU - Fernández, José M.

AU - Funahashi, Akira

AU - Gordon, Paul M.K.

AU - Goto, Naohisa

AU - Groscurth, Andreas

AU - Gutteridge, Alex

AU - Holland, Richard

AU - Kano, Yoshinobu

AU - Kawas, Edward A.

AU - Kerhornou, Arnaud

AU - Kibukawa, Eri

AU - Kinjo, Akira R.

AU - Kuhn, Michael

AU - Lapp, Hilmar

AU - Lehvaslaiho, Heikki

AU - Nakamura, Hiroyuki

AU - Nakamura, Yasukazu

AU - Nishizawa, Tatsuya

AU - Nobata, Chikashi

AU - Noguchi, Tamotsu

AU - Oinn, Thomas M.

AU - Okamoto, Shinobu

AU - Owen, Stuart

AU - Pafilis, Evangelos

AU - Pocock, Matthew

AU - Prins, Pjotr

AU - Ranzinger, René

AU - Reisinger, Florian

AU - Salwinski, Lukasz

AU - Schreiber, Mark

AU - Senger, Martin

AU - Shigemoto, Yasumasa

AU - Standley, Daron M.

AU - Sugawara, Hideaki

AU - Tashiro, Toshiyuki

AU - Trelles, Oswaldo

AU - Vos, Rutger A.

AU - Wilkinson, Mark D.

AU - York, William

AU - Zmasek, Christian M.

AU - Asai, Kiyoshi

AU - Takagi, Toshihisa

N1 - Funding Information: BioHackathon 2008 is financially supported by the Integrated Database Project, Ministry of Education, Culture, Sports, Science and Technology of Japan and the Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology, Japan.

PY - 2010/8/21

Y1 - 2010/8/21

N2 - Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.

AB - Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.

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U2 - 10.1186/2041-1480-1-8

DO - 10.1186/2041-1480-1-8

M3 - Review article

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VL - 1

JO - Journal of Biomedical Semantics

JF - Journal of Biomedical Semantics

M1 - 8

ER -

The DBCLS BioHackathon: Standardization and interoperability for bioinformatics web services and workflows

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